• Biotech Bits by Ricardo Vidal

    A diverse look at biotechnology from various angles

    • Bad Protocols for Dummies

      Wednesday, 12 Dec 2007 - 17:55 UTC

      There has been a lot of talk about making scientific openness and the benefits from disclosing research with the scientific community.

      One area of this openness that interests me is the disclosure of so called “bad protocols”. I’m still very new to science, but I know that a lot of researchers work hard on their projects and sometimes the theory just doesn’t match the reality and so, the mis-result brings them back to the drawing board.

      Failed experiments are taking place all the time, and a way to help out is make such information available to the scientific community.

      I saw the usefulness of such “no-no techniques” during a recent class where a professor told us to perform different steps than that of the protocol because he’d been there, and done that… and it wasn’t the best option.
      So, by telling us that he’d failed before, we didn’t have to and could use his new findings to move forward.

      This is just a small example of what I think could be a great resource. A “how to waste time in the lab” repository so researchers can avoid common pitfalls.

      This could be a repository online with all the usual web2.0 paraphernalia but would probably require some anonymity for those afraid of showing their “bad protocols” :)

      Last updated: Wednesday, 12 Dec 2007 - 17:55 UTC

      • Comments

        • Date:
          Wednesday, 12 Dec 2007 - 21:24 UTC
          john wilbanks said:

          +1 brilliant.

          (hey, we should be able to vote posts up and down here, too! /me pads off to corie’s blog to say so)

          However – lots of science happens when smart people ignore the “it can’t be done that way” argument. Technology improves, times change, and some things indeed become possible. So how do you build a list of bad protocols without creating more creaky “wisdom of the academy” against which rebellious scientists are judged and found wanting?

        • Date:
          Friday, 14 Dec 2007 - 01:42 UTC
          Pedro Beltrao said:

          Very nice :). Sharing negative protocols (and/or data in general) is a great use of the web but we are still far from having the right tools (easy to use) and the sharing mindset. I think most people would agree that it would be useful to know what other people tried and failed but like other ideas (unique IDs for authors, computer readable summary for papers, etc) they need a large number of people to move it along.

        • Date:
          Friday, 14 Dec 2007 - 18:11 UTC
          Ricardo Vidal said:

          I think this could be an interesting project to put together. It could start off as being an “alternative methods” type of repository where experienced scientists can share their views on certain certain lab techniques.
          This sharing of tricks-of-the-trade could lead to the so called negative protocols inadvertently.

          I’m going to think about how this could be technically be setup online. Don’t think wiki would be a good option. Maybe a submission form system with some sort of organization based on topics/tags/categories…

        • Date:
          Friday, 14 Dec 2007 - 19:36 UTC
          Deepak Singh said:

          Getting that critical mass is well … critical. One of my constant irritations as a student was learning the hard way what didn’t work. Now, that in itself is an educational experience, but sharing it can help others from not replicating your errors.

        • Date:
          Friday, 14 Dec 2007 - 20:33 UTC
          Ricardo Vidal said:

          It’s the mere saving of time, energy and material that really comes into play here. I can’t understand why something like this hasn’t been created already.

        • Date:
          Sunday, 23 Dec 2007 - 18:49 UTC
          Pedro Beltrao said:

          “I can’t understand why something like this hasn’t been created already.”
          Even if there is a clear advantage it takes some (small) energy from everyone to create these formal reports of negative results/protocols. The return is great since each one would benefit from the all others “small” amount of work. Its a no-brainer but still there is no clear way to organize everyone to do these things.
          The reward also depends on the amount of people already doing it. Why is delicious/digg/youtube/flickr so great? It is not really the technology behind the sites, it is the amount of people that reached enough critical mass to make these sites the best of their type.
          So the problem is not so much creating the website(s) but it is getting enough scientists to start using so that it is obvious to everyone else that is it useful and it snowballs from there.

        • Date:
          Thursday, 27 Dec 2007 - 06:46 UTC
          Deepak Singh said:

          Pedro is very right. It’s actually much the same for a number of things in the life sciences. Getting critical mass is very difficult. In many cases it is a niche area where the volume will never be enough, or in cases where the total volume should be sufficient, not enough people use the service to reach critical mass.

        • Date:
          Thursday, 27 Dec 2007 - 06:46 UTC
          Deepak Singh said:

          Pedro is very right. It’s actually much the same for a number of things in the life sciences. Getting critical mass is very difficult. In many cases it is a niche area where the volume will never be enough, or in cases where the total volume should be sufficient, not enough people use the service to reach critical mass.


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